[vtkusers] vtk 5.6.1 on a mac wrapped in Java
Mark Roden
mmroden at gmail.com
Wed Dec 8 22:21:20 EST 2010
So, any idea on how to fix this issue? Getting
ERROR: In /Users/mmroden/Documents/src/vtk-5.6.1/vtk-5.6.1/Filtering/vtkDemandDrivenPipeline.cxx,
line 802
vtkStreamingDemandDrivenPipeline (0x133f80aa0): Input for connection
index 0 on input port index 0 for algorithm
vtkImageChangeInformation(0x133f7fcc0) is NULL, but a vtkImageData is
required.
right after trying to run a vtkChangeImageInformation pipeline.
I tried this also using the straight vtk DICOM reader (rather than the
gdcm reader), and it gives the same error, but at a different point in
the app. Basically, anything that's pipeline-based appears to be
thinking that the inputs haven't been set, which is pretty much all of
the vtk stuff I have in there.
Thanks for any help,
Mark
On Thu, Dec 2, 2010 at 11:32 AM, Sebastien Jourdain
<sebastien.jourdain at kitware.com> wrote:
> the Unix makefile is fine.
> To setup release you just need to write Release in the CMake config
> for the build type (CMAKE_BUILD_TYPE).
> You can switch also the optimisation to -02 instead of -03 in the
> ..._FLAGS_RELEASE options.
>
> But I doubt that it could come from that.
>
> Seb
>
>
> On Thu, Dec 2, 2010 at 1:49 PM, Mark Roden <mmroden at gmail.com> wrote:
>> Maybe the problem is the build method I'm using for the libraries.
>>
>> I'm building both gdcm and vtk using Unix makefiles on the mac, since
>> the xcode stuff isn't working.
>>
>> How can I make sure that I'm building release versions on both
>> machines? There's a suggestion here:
>> http://comments.gmane.org/gmane.comp.lib.mitk.user/1052
>>
>> that this bug could be due to compilation problems.
>>
>> Specifically, I'd like for 64 bit release versions to be made. On
>> XCode, that's a dropdown selection, but typing 'make release' results
>> in 'don't know how to build release, stop', and I'm not sure what
>> 'make all' is doing.
>>
>> Thanks,
>> Mark
>>
>> On Thu, Dec 2, 2010 at 7:00 AM, Mark Roden <mmroden at gmail.com> wrote:
>>> The java code works fine on windows, it's the same code, shared via
>>> git on the different machines
>>>
>>> I'm not trying to inherit. vtkImageChangeInformation is exposed by
>>> the vtk java wrapping, but the vtlImageData I'm passing in isn't
>>> working.
>>>
>>> This code works in java on windows. It doesn't on mac. I use the
>>> same libraries underneath, or at least, the same versions of gdcm and
>>> vtk are built and used.
>>>
>>> On Thu, Dec 2, 2010 at 6:53 AM, Sebastien Jourdain
>>> <sebastien.jourdain at kitware.com> wrote:
>>>> I was talking about your Java code that was using VTK, not VTK itself.
>>>>
>>>> Moreover, I think that you can not inherit from VTK classes in Java...
>>>>
>>>> Seb
>>>>
>>>> On Thu, Dec 2, 2010 at 9:17 AM, Mark Roden <mmroden at gmail.com> wrote:
>>>>> Hi Sebastien,
>>>>>
>>>>> I can't use the windows binary on the mac-- the vtk underpinnings are
>>>>> still C++, which means that it's compiled into a dll on windows, which
>>>>> means (as far as I know, and as my experiments confirm), it doesn't
>>>>> work on a mac. I have to recompile vtk for the mac directly. The
>>>>> java wrappings (the jar) should be identical, though. Just to be
>>>>> safe, I'm using the mac-generated jars now.
>>>>>
>>>>> I am sure that the filenames have no spaces or special strings. If
>>>>> you look at the line
>>>>>
>>>>> String theString2 = sortedFT.get(i)
>>>>>
>>>>> I can stop there with the debugger and see the contents of the string,
>>>>> and it's clean.
>>>>>
>>>>> For what it's worth, Fred Fred asked about this error message a year
>>>>> ago, and he got no response:
>>>>> http://public.kitware.com/pipermail/vtkusers/2009-October/102935.html
>>>>> I don't know if he was in the same situation as me, though.
>>>>>
>>>>> Thanks,
>>>>> Mark
>>>>>
>>>>> On Thu, Dec 2, 2010 at 5:02 AM, Sebastien Jourdain
>>>>> <sebastien.jourdain at kitware.com> wrote:
>>>>>> Hi Mark,
>>>>>>
>>>>>> did you try your windows (Java) binary on your mac to see if you get
>>>>>> the same behavior ?
>>>>>> Are you sure that on your mac, the filename provided to the reader are
>>>>>> correct ? (no space or special string ?)
>>>>>>
>>>>>> Seb
>>>>>>
>>>>>> On Thu, Dec 2, 2010 at 12:01 AM, Mark Roden <mmroden at gmail.com> wrote:
>>>>>>> Hi all,
>>>>>>>
>>>>>>> So I managed to get vtk 5.6.1 to work on a mac with java wrappings on
>>>>>>> (10.6.5) and with gdcm.
>>>>>>>
>>>>>>> The following code is producing errors that I don't see on windows:
>>>>>>>
>>>>>>> IPPSorter sorter = new IPPSorter();
>>>>>>> sorter.SetComputeZSpacing(true);
>>>>>>> sorter.SetZSpacingTolerance(0.000001);
>>>>>>> Boolean sorted = sorter.Sort(theSeriesFiles);
>>>>>>> //sorter.Sort(ft);
>>>>>>>
>>>>>>> //have to make a vtk string array
>>>>>>> FilenamesType sortedFT = sorter.GetFilenames();
>>>>>>> long theSize = sortedFT.size();
>>>>>>> vtkStringArray sa = new vtkStringArray();
>>>>>>> for (int j = 0; j < theSize; j++) {
>>>>>>> String theString2 = sortedFT.get(j);
>>>>>>> sa.InsertNextValue(sortedFT.get(j));
>>>>>>> }
>>>>>>> gdcmReader.SetFileNames(sa);
>>>>>>>
>>>>>>> gdcmReader.Update();
>>>>>>>
>>>>>>> imageData = gdcmReader.GetOutput();
>>>>>>>
>>>>>>> //make sure that we're getting spacing and orientation info
>>>>>>> double[] spacing = imageData.GetSpacing();
>>>>>>> spacing[2] = sorter.GetZSpacing();
>>>>>>> imageData.SetSpacing(spacing);
>>>>>>> double[] origin = imageData.GetOrigin();
>>>>>>> double[] bounds = imageData.GetBounds();
>>>>>>> double[] extraOrigin = {0,0,0};//because vtk will only
>>>>>>> flip about 0,0,0
>>>>>>>
>>>>>>> vtkImageChangeInformation imageSpacingChange = new
>>>>>>> vtkImageChangeInformation();
>>>>>>> imageSpacingChange.SetInput(imageData);
>>>>>>> imageSpacingChange.SetOutputSpacing(spacing[0],
>>>>>>> spacing[1], spacing[2]);
>>>>>>> imageSpacingChange.SetOutputOrigin(extraOrigin);
>>>>>>> imageSpacingChange.Update();
>>>>>>>
>>>>>>> Once the last line is hit, the following error is reported in netbeans:
>>>>>>>
>>>>>>> ERROR: In /Users/mmroden/Documents/src/vtk-5.6.1/VTK-5.6.1/Filtering/vtkDemandDrivenPipeline.cxx,
>>>>>>> line 802
>>>>>>> vtkStreamingDemandDrivenPipeline (0x135884c10): Input for connection
>>>>>>> index 0 on input port index 0 for algorithm
>>>>>>> vtkImageChangeInformation(0x1358853c0) is NULL, but a vtkImageData is
>>>>>>> required.
>>>>>>>
>>>>>>> This code works perfectly well in Windows, and the spacing, origin,
>>>>>>> and bounds arrays all match the values in windows when loading the
>>>>>>> same series there. So, I know that the gdcm side of things is
>>>>>>> working, at least to the point that those arrays are being reported
>>>>>>> correctly.
>>>>>>>
>>>>>>> Because the pipeline is breaking there, nothing else is working. What
>>>>>>> can I do to fix it?
>>>>>>>
>>>>>>> Thanks,
>>>>>>> Mark
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>>>>>>>
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>>>>>>
>>>>>
>>>>
>>>
>>
>
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